Transcriptome Analysis of the <i>CML</i> Gene Family in <i>Bletilla striata</i> and Regulation of Militarine Synthesis Under Sodium Acetate and Salicylic Acid Treatments by Kunqian Li, Mengwei Xu, Qingqing Li, Hongwei Li, Ya Xu, Delin Xu

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Trophoblast cell response to periodontal pathogens unveils oxidative stress networks between periodontitis and pre-eclampsia: Mendelian randomization, transcriptomic analysis, and... by Lihua Hu, Shuqin Liu

“…Transcriptomic analysis of public data sets identified cross-talk genes and oxidative stress markers. …”
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Histological and transcriptome analysis provides new insights into the hematopoietic and immune functions of head kidney, trunk kidney and spleen of adult large yellow croaker, Lar... by Aihua Zhong, Yingbin Wang, Haiqi Zhang, Xiaojun Yan, Shuo Jia

“…This study provides a comprehensive histological and transcriptomic analysis of these organs in adult large yellow croaker, revealing their normal physiological roles in hematopoiesis and immunity. …”
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Multi-tissue transcriptomic analysis reveals that L-methionine supplementation maintains the physiological homeostasis of broiler chickens than D-methionine under acute heat stress... by Mingyung Lee, Hyesun Park, Jung Min Heo, Ho Jun Choi, Seongwon Seo

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Integrated analysis of transcriptomics and metabolomics and high-throughput amplicon sequencing reveals the synergistic effects of secondary metabolites and rhizosphere microbiota... by Li Yingtao, Li Qiaofeng, Wang Lijuan, Qi Shuyun, Jiang Zhou, Zhang Wenping, Zhang Aili

“…In this study, we utilized an integrated analysis of transcriptomics, metabolomics, high-throughput amplicon sequencing, and culturomics for revealing the difference of healthy samples (CH) and diseased samples (CD) and studying the defense mechanism of P. tunicoides in resisting root rot. …”
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The Molecular Mechanisms Underlying Zucchini-Induced Changes in the Host Adaptation of Cotton- and Cucumber-Type <i>Aphis gossypii</i> by Yibin Pan, Weili Xu, Li Wang, Kaixin Zhang, Jichao Ji, Dongyang Li, Xiangzhen Zhu, Xueke Gao, Junyu Luo, Jinjie Cui

“…Our investigation revealed that both Hap1 and Hap3 <i>A. gossypii</i> underwent significant body size enlargement following host transfer to zucchini. Transcriptomic analysis revealed that zucchini-mediated host adaptation in the <i>A. gossypii</i> biotypes (Hap1/Hap3) involves insulin metabolism and detoxification pathways, with 17 co-differentially expressed genes (e.g., <i>Col-I</i> (type I collagen), <i>CYP450 6a13</i>, <i>peroxidase</i>) potentially critical for adaptation. …”
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Bordetella pertussis infection activates the type I interferon signaling pathway to exacerbate respiratory tract inflammatory response by Wenwen Jiang, Wenwen Jiang, Jiangli Liang, Lukui Cai, Jingyan Li, Qin Gu, Yan Ma, Mingbo Sun, Xin-an Jiao, Li Shi, Li Shi

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Gold Nanoparticles Functionalized With 5-Amino-2-Mercaptobenzimidazole: A Promising Antimicrobial Strategy Against Carbapenem-Resistant Gram-Negative Bacteria by Zhang J, Zhang X, Yao Z, Pan J, Ye J, Xia P, Zhou T, Cao J

“…Keywords: carbapenem-resistant gram-negative bacteria, benzimidazole, gold nanoparticles, biocompatibility, transcriptome analysis…”
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Integrative immunology identified interferome signatures in uveitis and systemic disease-associated uveitis by Danielle Dias Munhoz, Dennyson Leandro M. Fonseca, Igor Salerno Filgueiras, Haroldo Dutra Dias, Helder I. Nakaya, Igor Jurisica, Igor Jurisica, Igor Jurisica, Hans D. Ochs, Hans D. Ochs, Lena F. Schimke, Luiz Vicente Rizzo, Otavio Cabral-Marques, Otavio Cabral-Marques, Otavio Cabral-Marques, Otavio Cabral-Marques, Otavio Cabral-Marques, Otavio Cabral-Marques

“…However, the global signature of type I, II, and III interferon-regulated genes (Interferome) remains largely uncharacterized in uveitis.MethodsIn this study, we conducted an integrative systems biology analysis of blood transcriptome data from 169 non-infectious uveitis patients (56 isolated uveitis, 113 systemic disease-associated uveitis) and 82 healthy controls.ResultsModular co-expression analysis identified distinct cytokine signaling networks, emphasizing interleukin and interferon pathways. …”
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Distinct characteristics of brain metastasis in lung adenocarcinoma: development of high-confidence cell lines by Jintao He, Zen-ichi Tanei, Dao-Sian Wu, Lei Wang, Yoshitaka Oda, Masumi Tsuda, Shinya Tanaka

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Altered aminoacid and lipid metabolism in a rat orofacial inflammation model determined by omics approach: potential role in trigeminal sensitisation by Krisztina Takács-Lovász, Timea Aczél, Violetta Mohos, Máté Harmath, Jennet Pirkuliyeva, Gellért Karvaly, Róbert Farkas, Michal Ciborowski, Joanna Godzien, Kata Bölcskei, József Kun, Zsuzsanna Helyes

“…Conclusions Integrated joint pathway analysis of metabolomic and transcriptomic data provides a useful approach to determine pathophysiological mechanisms of trigeminal sensitization and identify novel drug targets for orofacial pain and headaches.…”
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Gene expression profiling in pure neural leprosy: insights into pathogenesis and diagnostic biomarkers by Mariana Martins de Athaide, Thyago Leal-Calvo, Tatiana Pereira Da Silva, Thabatta Leal Silveira Andrezo Rosa, Helen Ferreira, Bernardo Miguel de Oliveira Pascarelli, Ana Caroline Siquara de Sousa, Marcia Rodrigues Jardim, Marcia Rodrigues Jardim, Marcia Rodrigues Jardim, Marcia Rodrigues Jardim, Marcia Rodrigues Jardim, Roberta Olmo Pinheiro, Roberta Olmo Pinheiro, Roberta Olmo Pinheiro

“…These findings may guide early diagnosis and improve patient outcome.MethodsIn the present study, we investigated the gene profiling of nerve samples from patients with PNL and revealed significant transcriptomic alterations compared to non-leprosy controls.ResultsPrincipal Component Analysis (PCA) of the 500 most differentially expressed genes separated the groups, with 1,199 genes showing differential expression (|log2FC| ≥ 1, FDR ≤ 0.1). …”
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Targeting PDCD4 in cancer and atrial fibrillation: mechanistic insights from integrated multi-omics and single-cell analysis by Juledezi Hailati, Zhiqiang Liu, Lei Zhang, Muhuyati Wulasihan

“…This work seeks to discover PDCD4-associated critical genes and clarify their regulation processes.MethodWe built a protein-protein interaction (PPI) network to emphasize important biological interactions and used transcriptome analysis to find differentially expressed genes (DEGs). …”
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Multiomics-based analysis of key genes, metabolites and pathways unveils mechanism associated with social rank in Chickens by Mengqiao Zhao, Limin Xing, Yushan Li, Jiaxin Zhang, Yinghui Liu, Fei Ye, Siyu Chen

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Mechanistic Exploration of Yiqi Zengmian in Regulating the Microenvironment as an Immunopotentiator with the Beijing Bio-Institute of Biological Products Coronavirus Vaccine Based... by Zeyue Yu, Yudong Wang, Jianhui Sun, Xiaotong Zheng, Liyu Hao, Yurong Deng, Jianliang Li, Zongyuan Li, Zhongchao Shan, Weidong Li, Yuling Qiao, Ruili Huo, Yibai Xiong, Hairu Huo, Hui Li, Longfei Lin, Hanhui Huang, Guimin Liu, Aoao Wang, Hongmei Li, Luqi Huang

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Genome-wide analysis of the CML gene family and its response to cold stress in Curcuma alismatifolia by D. Ying, R. Jintong, W. Yang, F. Zuhong, T. Tian, Z. Hong

“…Promoter regions were enriched with cis-acting elements associated with growth and development, biotic/abiotic stress responses, and hormone responsiveness, suggesting diverse functional roles for CACML genes. Transcriptome analysis indicated that CACML140 regulates the cold stress response in Curcuma alismatifolia via the MAPK cascade signaling pathway. …”
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Analysis of the Differences Among <i>Camellia oleifera</i> Grafting Combinations in Its Healing Process by Zhilong He, Ying Zhang, Chengfeng Xun, Zhen Zhang, Yushen Ma, Xin Wei, Zhentao Wan, Rui Wang

“…The results demonstrated that Comb. 4 (Xianglin 27 rootstock) exhibited superior compatibility, characterized by systemic antioxidant activation (peaking at 4–8 DPG), rapid auxin accumulation (4 DPG), and efficient sugar allocation. Transcriptome sequencing and WGCNA analysis identified 3781 differentially expressed genes, with notable enrichment in stress response pathways (Hsp70, DnaJ) and auxin biosynthesis (YUCCA), while also revealing key hub genes (FKBP19) associated with graft-healing efficiency. …”
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Research on the pathogen causing root rot on Phyllanthus emblica from the perspectives of identification, bionomics, fungicide sensitivity assay, and transcriptome analysis under d... by Yiming Zhang, Minyan Song, Minyan Song, Yonghong He, Yehua Si

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Integrative Identification of Chloroplast Metabolism-Related RETICULATA-RELATED Genes in Soybean by Qianli Dong, Lu Niu, Xiyu Gong, Qianlong Xing, Jie Liang, Jun Lang, Tianya Wang, Xiangdong Yang

“…Expression profiling across fourteen tissues and three abiotic stress conditions revealed a dynamic shift in expression levels between leaf-predominant and root-enriched <i>GmRER</i> paralogs after stress treatments. A comparative transcriptome analysis of six soybean landraces further revealed transcriptional polymorphism in the <i>GmRER</i> family, which was associated with the expression patterns of lipid biosynthesis regulators. …”
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Deciphering transcriptomic signatures in schizophrenia, bipolar disorder, and major depressive disorder by Priyanka, Rajesh Kumar, Vinod Kumar, Ashwani Kumar, Sandeep Singh Rana

“…Our comprehensive transcriptomic analysis reveals both shared molecular mechanisms and distinct immune signatures across schizophrenia, bipolar disorder, and major depressive disorder, advancing our understanding of psychiatric pathophysiology while highlighting the heterogeneous nature of these conditions. …”
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